MolNFT v1 · #177676 · protein

Overall structure of erastin-bound xct-4F2HC complex

7EPZ · 4F2 cell-surface antigen heavy chain: “Overall structure of erastin-bound xct-4F2HC complex”. Electron microscopy, 3 ligands (PX8, J9O, NAG), 12 pockets (best druggability 0.74). MolNFT v1 #177676 on GenesisL1: 3D structure, binding…

PDB: 7EPZ
Type: protein
Length: 921 residues
Chains: 2
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 4F2 cell-surface antigen heavy chain; CYSTINE/GLUTAMATE transporter
UniProt: J3KPF3, Q9UPY5
Ligands: PX8, J9O, NAG
Pockets: 12 · best druggability 0.74

Structure

electron microscopy · 2 distinct chains · 46% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	4F2 cell-surface antigen heavy chain	protein	468	29% helix, 15% strand	J3KPF3
B	CYSTINE/GLUTAMATE transporter	protein	453	63% helix, 1% strand	Q9UPY5

Ligands and binding sites

PX8 · 1,2-distearoyl-sn-glycero-3-phosphate · ligand · 2 copies · chains A, B
J9O · 2-[(1S)-1-[4-[2-(4-chloranylphenoxy)ethanoyl]piperazin-1-yl]ethyl]-3-(2-ethoxyphenyl)quinazolin-4-one · ligand · chains B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	551	0.74	0.82	60	J9O
2	722	0.68	0.76	63	empty
3	87	0.64	0.90	22	empty
4	374	0.63	0.78	24	PX8
5	231	0.61	0.81	24	empty

Interfaces

1 interface between chains.

A–B · 1209 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 glycan, 1 disulfide (N-glycosylation, disulfide).

Compared structures

7EPZ · Overall structure of Erastin-bound xCT-4F2hc complex · the same entry in another collection · chain A against A, TM-score 1.00
Q9UPY5 · AlphaFold monomer V2.0 prediction for CYSTINE/GLUTAMATE transporter (Q9UPY5) · a predicted model of the same protein · chain B against A, TM-score 0.92

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt J3KPF3
Every structure of UniProt Q9UPY5
Elsewhere: RCSB PDB 7EPZ · PDBe 7EPZ · UniProt J3KPF3 · UniProt Q9UPY5

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